I went for the Invis pool on my stalker purely for Phase Shift which I have to admit is pretty handy for those times when things get a tadge too much - Pahse Shift -> Flee - works wonders 
Golden-Phoenix - Lvl 50 Fire/Fire Tank
Oodja Nikabolokov - Lvl 50 SS/WP Brute
Baby-Phoenix - Lvl 50 Peacebringer
How much wood would a woodchuck chuck if a woodchuck could Chuck Norris?
Stealth + Hide + IO Stealth in travel power also puts you at the Stealth cap which is pretty useful if you plan to PvP, if you are PVE then hide on it's own is fine (but as you say phase shift is pretty handy)
Other than that Stamina (as with most characters) as if you are out of endurance you're dead.
Yeah true - I survived without Stamina until about lvl 40 but at that point I started to really struggle - it is OK for when you are using the age old 'AS + Run' technique but for longer battles end becomes a problem!
Golden-Phoenix - Lvl 50 Fire/Fire Tank
Oodja Nikabolokov - Lvl 50 SS/WP Brute
Baby-Phoenix - Lvl 50 Peacebringer
How much wood would a woodchuck chuck if a woodchuck could Chuck Norris?
Personally i like to maximize defense to improve stalker survivability so i would be thinking in those area's altho stealth and Invis do offer extra Def i don't think the end drain is worth it in PVE altho some might get some usage from phase shift but i find it situational preferring to pick something from my primary or secondary that i would use more often.
I stick to Combat jumping/Super jump for my melee toons basically because it offers the best combat mobility with extra def from CJ.
Hasten from the speed power pool is always a good choice i feel aswell as fitness for the all important stamina.
IO's altho optional do offer the best way to improve a charactor especially the defense.
My basic train of thought is to improve defense without impacting my scrapability or end usage and sticking to powers i would use often.
Defiant's GoEH/MILITIS METUS
Hi currently play my lvl 15 stalker captain communist which I find great fun. I already have claws and nin jitsu as well as flight so wondering if theres any other pools i should get/worth getting. I was thinking about invisibility?
cheers